Admin: Pierre Lindenbaum

Reputation:
94,680
Status:
Trusted
Location:
France/Nantes/Institut du Thorax - INSERM UMR1087
Website:
http://plindenbaum.blo...
Twitter:
yokofakun
Scholar ID:
Google Scholar Page
Last seen:
2 hours ago
Joined:
7 years, 4 months ago
Email:
p**********@yahoo.fr

Posts by Pierre Lindenbaum

<prev • 5,939 results • page 2 of 594 • next >
2
votes
1
answer
106
views
1
answers
Answer: A: Extract parts of reads from BAM file that overlap a specific region of genome
... using [samjs][1] : samtools view -bu -F 4 file.bam chr1:13974-22442 |\ java -jar dist/samjs.jar -e 'record.alignmentStart <= 13974 && record.alignmentEnd >= 22442' see also : https://www.biostars.org/p/150530/ [1]: http://lindenb.github.io/jvarkit/SamJavascript.html ...
written 1 day ago by Pierre Lindenbaum95k
0
votes
1
answer
87
views
1
answers
Answer: A: delete IDs from a list file
... use a **Makefile** to only compute the remaining things. Something like sampleIDs=$(shell ls *.fastq | cut -d '.' -f 1 | sort | uniq) define run $(1).txt: $(1).R1.fq $(1).R2.fq echo $$^ > $$@ endef all: $(addsuffix .txt,${sampleIDs}) $(eval $(foreach S,${sampl ...
written 1 day ago by Pierre Lindenbaum95k
1
vote
0
answers
81
views
0
answers
Comment: C: search a large dbsnp file using another most efficiently
... please sort your files on the desired columns and add a test for **[join][1]** [1]: https://linux.die.net/man/1/join ...
written 1 day ago by Pierre Lindenbaum95k
0
votes
1
answer
103
views
1
answers
Comment: C: How to view the contents and header of a Vcf file in linux using VCFTOOLS
... If this answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. ![Upvote|Bookmark|Accept][1] [1]: http://i66.tinypic.com/14xdmh2.jpg ...
written 1 day ago by Pierre Lindenbaum95k
0
votes
1
answer
103
views
1
answers
Answer: A: How to view the contents and header of a Vcf file in linux using VCFTOOLS
... gunzip -c ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz ...
written 1 day ago by Pierre Lindenbaum95k
0
votes
5
answers
181
views
5
answers
Comment: C: Run Samtools on multiple files
... > does that "16" means the no. of threads? yes ...
written 3 days ago by Pierre Lindenbaum95k
3
votes
5
answers
181
views
5
answers
Answer: A: Run Samtools on multiple files
... create the following '**Makefile**' SHELL=/bin/bash BAMS=$(shell ls -1 *.bam) define run $$(addsuffix .sorted.bam,$$(basename $(1))): $(1) samtools sort $$< $$(basename $$@) samtools index $$@ endef all: $(addsuffix .sorted.bam,$(basename ${BAMS})) ...
written 3 days ago by Pierre Lindenbaum95k
0
votes
0
answers
109
views
0
answers
Comment: C: bbnorm Java error?
... I was asking for the version of bbnorm ...
written 4 days ago by Pierre Lindenbaum95k
0
votes
0
answers
109
views
0
answers
Comment: C: bbnorm Java error?
... which version is it ? ...
written 4 days ago by Pierre Lindenbaum95k
1
vote
2
answers
136
views
2
answers
Comment: C: tabix for ID column
... yes because join optimize the fact that the file is sorted: it will ignore everything before rs1234 and stop after rs1234. of course , for speed you would use: LC_ALL=C grep -w '^rs1234' but you don't know is there is more than one occurence of rs1234 in the file (it happens) grep -w - ...
written 4 days ago by Pierre Lindenbaum95k

Latest awards to Pierre Lindenbaum

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Scholar 4 days ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs
Appreciated 4 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 4 days ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Student 5 days ago, asked a question with at least 3 up-votes. For Exome Aggregation Consortium (ExAC) database ?
Good Answer 5 days ago, created an answer that was upvoted at least 5 times. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Appreciated 5 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Scholar 5 days ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs
Appreciated 6 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Popular Question 7 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Scholar 8 days ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs
Appreciated 11 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Scholar 12 days ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs
Scholar 12 days ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs
Appreciated 12 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Scholar 14 days ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Poly A Sequences In Small Rna

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 665 users visited in the last hour